Chuck vs Season 3
by Sunflower90
Summary: So, this is what I think is going to happen in season 3. Based on my own speculation as well as what was said at SDCC and some spoilers that are coming out.
1. Chapter 1

Disclaimer: I don't own Chuck or any of the characters.

Chuck vs. The Realization

Sarah held Chuck's hand as they walked down the beach in the sunset. They said nothing, just basked in each other's presence. This was what he always wanted and more. "Chuck," she said. "Chuuuuuuuuuck." And then she slapped him. Wait, what?

"Chuck, oh my God, Chuck, wake up!" Sarah was shouting at him. Great, he thought, it was just a dream. As he came to slowly, he realized he was lying on a cot in Castle and Sarah was bent over him. "Sarah, what is going on," he asked. "Chuck, you uploaded the new Intersect, don't you remember?" Now it was all rushing back to him. Bryce lying dead on the floor, all of the new images, the Kung Fu. "I'm the Intersect again," he said, not sounding as sure as felt when he had uploaded it. Sarah looked very angry for some reason. "Why so grumpy?" he said in a teasing voice while sitting up. But she was in no mood to play. "Why do you think? You could have just walked away and had your life, but you couldn't do that," said Sarah. "You said I was a hero, and without the Intersect I didn't feel like one. And I knew I wouldn't be able to help you guys fight those Ring baddies without it. I didn't know about the Kung Fu," he replied.

Sarah had to turn away from him at this point. She had been willing to give up everything she had worked for in her life so that she could be with him and finally be happy, but he had just gone and thrown that all away. She didn't want him to see the pain and hurt in her eyes. She had to get it together. "You never listen, Chuck. I was going to tell you something back at the reception." She was on the brink of tears, barely able to hold them back. Then Chuck remembered what Bryce had said: "She wasn't going to come." Sarah had wanted to stay with him. She wanted to live a normal life with the normal Chuck Bartowski. "Bryce... Bryce told me before he... You weren't going to leave with him, were you?" She shook her head 'no'. "Sarah, I'm so sorry I screwed this all up. I just didn't realize what Bryce was saying at the time. I wanted to be a hero, for you. I thought you would want that." "You will always be a hero to me, whether you have a super computer brain or not. That is why I was going to stay. But Chuck, this does put a dent in my plans."

Everything was different now. "Where do we go from here," he asked her. "I don't even know," she replied," but we do need to contact the General. You obviously have something very powerful in your head. You took out five Ring agents, who knows what kind of damage you could do." Now he was worried. He never thought he could hurt someone. "Sarah," he said in that sweet little voice of his,"may I sleep while you talk to the General. I'm still feeling a tad worn out." She couldn't resist that voice or the adorable puppy dog voice. "Sure."

While he went back to sleep, she went out to talk to the General. "General, we have some new developments." "I already head from Colonel Casey at the Intersect building where he is cleaning up. Walker, you and Bartowski have some serious explaining to do," she growled back at the agent. "General, Chuck has uploaded the new Intersect and seems to know Kung Fu as well. General, he did this without permission from anyone, and is quite remorseful. He has destroyed the computer as well, but he is now back in as much danger or more than before. What kind of changes were made to the new Intersect," asked Sarah, slightly scared to hear the answer. "This new Intersect is extremely powerful. It creates a super agent, someone stronger and more ruthless than anyone. But it has some side effects. It is affected by emotions. Because it was built for Agent Larkin, who is trained to not let emotions dictate his actions, we weren't really worried about that. But now, Chuck's emotional side could make the new Intersect and Chuck very dangerous. I will send you a file containing pertinent information. In the meantime, watch Chuck. See in what ways the Intersect manifests itself. And at all costs, protect others from him. He may strike at any moment. Good day and good luck, Walker." And with that her picture disappeared from the screen.

Sarah let Chuck sleep another two hours. When she woke him it was just after midnight. "Chuck, I want you to stay at my place tonight. I know you were going to stay with Morgan, but with the new developments I think it would be best if you came with me." He didn't protest. They left the Castle and got Chuck's bag from the Herder and Sarah took them back to her hotel.

"Sarah, what does this new Intersect do exactly," Chuck asked as they walked into her room. "I don't much yet, but the General said it is very dangerous. We'll know more tomorrow when we get the file on it. For now, you should just relax," she replied. He looked around the room uncomfortably and clutched his bag with both hands. "Ummm, there is only one bed." "Chuck, we've been over this. I don't mind sharing a bed with you." She was a little bit embarrassed to be so forward, but she wanted to get her way at least once today. "I just wanted to give you the option, you know, if you changed your mind," he said, still slightly red in the face. She loved how chivalrous he was. "Why don't you get ready for bed in the bathroom. I already showered back at Castle, so take as long as you need. I'll talk to you in the morning." He turned and walked into the bathroom with his things very obediently, but not before walking over to her and planting a gentle kiss on her cheek. "Thanks... for everything." She smiled as she watched him walk away.

While he was in the shower, she had some time to think. Did this mean that they would never be together? Will he be an agent or an asset? Would it matter which one? She didn't think it was okay to get involved with an agent, but she did with Bryce. She would just have to sleep on it. Too much had happened today. About 30 minutes later, he slipped into bed beside her. She was still awake; her mind wouldn't shut off, but he didn't know that. "'Night, Sarah. I'm so sorry. I love you, and I didn't mean to hurt you." Then he kissed the back of her neck, cuddled up next to her and fell into a deep sleep. With him beside her, she was able to as well.


	2. Chapter 2

Disclaimer: Don't own the characters or Chuck at all. Sucks, right?

Chuck vs. the Incident

After that first night together, Chuck and Sarah decided it would be better for them to both stay at Chuck's place. Ellie and Awesome had left for their honeymoon that morning and would be gone for two weeks. Sarah needed to stay with him so they could continue his training. She also needed protect him and protect others from him. They were still very unsure about how powerful the new Intersect was, and they were unable to find Chuck's dad who could explain so much. He had disappeared after the wedding and no one knew where he was.

Castle had turned into an extremely advanced training facility complete with a full dojo and combat simulator. Beckman had ordered Casey and Sarah to test Chuck on his abilities, but to be careful. Chuck was extremely strong. On Chuck's first day of training he was hesitant. "Casey, I can't just hit you. I don't think it works like that. I have to be provoked, you know, think you're a threat." This was like music to Casey's ears. He could say all of the things to the twerp he had been holding in these past two years. "Hey, moron, if you don't grow a pair I'm going to have ask your girlfriend to let you borrow hers. At least she can kill people," said Casey with a grunt for added effect. "Now that is just making me feel depressed not threatened. You actually have to do something," Chuck replied. So Casey lunged at him, and Chuck saw the moves play out in his flash. He deflected Casey's first blow then countered with a strong right hook. Then he delivered an epic kick to Casey's chest which knocked the colonel to the ground breathless. Chuck's flash subsided when he observed that his attacker had been neutralized. "Chuck, that was incredible," Sarah said, going over to help Casey. Chuck smiled. All he had wanted to do with this new Intersect was make her happy and proud of him. He wanted to be the man she thought he was. "Nice shot, moron," said Casey breathlessly, "but next time you're not going to get so lucky." "Dude, I have a computer in my head. I'll be able to beat you every time. I pwned five agents at once. I'm sure I can take you," Chuck replied, chest puffed out.

The rest of the day was spent in the shooting range teaching Chuck about guns, seeing as more combat with Casey would be dangerous to the Marine's spirit and body. Chuck flashed on the Sig Sauer P226 9mm when he first saw it, which taught him how to shoot it, but he still had a lot to learn. Like which gun was best for what situation. All of this his handlers stood by his side and taught him. Sarah found any excuse she could throughout the day to brush up against him or hold his hand. While she was angry with him at first about the re- upload, now it was kind of sexy. She was beginning to understand why he wanted to do this. The things that she like about Bryce (his arch nemesis), like the way he fought or how he looked holding a gun, were now part of Chuck too. It hurt her a little to compare Bryce and Chuck, but she just took it as part of her grieving process.

When they went home that night, Chuck was exhausted. "I can make you dinner if you want. Or you can order something," said Sarah. She had been so attentive to him all day, and he thought it was kind of fishy. "We can just order pizza. I don't want you to have to make me something and clean it up. It's way too much trouble," he replied. So they ordered a pizza and sat on the couch watching a movie until Sarah fell asleep with her head in his lap. This was the best feeling in the world. For the first time in a long time, it felt so real, so normal. When Chuck looked down at Sarah, she had a smile on her face. He ran his fingers through her golden hair. She let out a soft sigh. Chuck decided it would be best if they slept in the bed and not on the couch, so he scooped her up in his arms and carried her to the bed. Sarah woke up when he picked her up, but wasn't about to let on. She really liked this. He was in attentive boyfriend mode. For a second she remembered why she had been so angry when Chuck re- uploaded the new Intersect, but forgot it the second his lips touched hers for a goodnight kiss. At least she was able to be with him.

The next day, Casey was not feeling well enough to fight Chuck again, so the General ordered Sarah to test Chuck's abilities. This was something she was looking forward to. She had loved it when she and Bryce (him again?) sparred. Hand to hand combat really turned her on. They had decided to make it as real as possible. Sarah would keep the knives strapped around her ankles and the gun tucked in the back of her pants. Casey would sit on the sidelines to prevent any major catastrophes. To begin the exercise Sarah would threaten Chuck with her gun drawn, hopefully provoking a flash. She took her gun out and aimed it at him. "All right, Mr. Bartowski," she said, "I hope you've said your goodbyes because you aren't going to be making it home tonight." "Sarah, I'm not flashing. I don't know what it is. My other flashed have come when people I cared about have been threatened, though. Maybe you should say something along those lines." He didn't want to fight Sarah, but she had seemed very excited to fight him. If it made her happy, then he was willing to do it. "Well then," she started again, "it's too bad you're going to have to die, leaving your sister and pretty little girlfriend all alone. I'll be by to see them after I'm done here with you." Then Chuck flashed. It was the most intense experience of his life. When he looked back at his assailant, he didn't see Sarah Walker. He saw a target, a threat. In a second he was lunging at her, fists drawn. He delivered calculated blows to her face and abdomen then knocked the gun from her hands. She did the best she knew how to counter them, but it was no use. She was highly over matched. Then Chuck went for the knives in her ankle. She was able to get them out of her hands before they struck her, but she was now beginning to feel she was in real danger. This wasn't Chuck. This person was a machine. But she didn't want to get Casey right away. He could get hurt, too, and she was pretty sure she still had a shot. That was until Chuck found the gun. He picked it up from the ground, went back to her, and pinned her to the ground. Chuck pressed the barrel to his girlfriend's forehead and tightened his grip on the handle.


	3. Chapter 3

Disclaimer: I don't own Chuck, silly.

A/N: Thank you to everyone for being patient with me. School is just taking far more time than I thought it would. I know this is short, but it should move the story forward for the time being. Also, heard that Chuck might be coming back far sooner than planned due to the failure of several NBC shows! Praying.

Accident

Sarah's heart was pounding in her chest. She didn't know what to do. In a split second, Casey came sneaking up behind Chuck. Charging him would just force him to shoot. Sarah's eyes widened and she let out a small breath, looking deep into Chuck's eyes. She was silently pleading with him to recognize her, to stand down. At that moment, something in Chuck snapped. He was out of the flash. He looked at his hand and looked at Sarah. "Ohmigod, ohmigod, ohmigod," he said over and over. "What have I done? What am I doing?" That's when Sarah broke for the first time in front of him. She began sobbing. This is exactly what she didn't want to happen. She had wanted a normal life with the man she loved, and he had ruined it. Chuck reached out to touch her, to comfort her, but she shrank back. He had nearly ended her life.

Casey took this time to deck Chuck square across the face. "Okay, I obviously deserve that," Chuck said from the floor. "Know we know why Bryce wanted this thing destroyed," Casey replied. "It got into your hands and look at the damage it's doing." Casey walked over and picked Sarah off the ground and brought her to the corner. "Hey, are you going to be all right? That was really intense there," Casey said trying to comfort his partner. "I... just... yeah, Casey. I'm fine," she finally choked out between tears, "I guess." Sarah's mind was reeling. She never thought that this could happen, that the intersect could turn him against her. And to top it all off she couldn't stop crying. She blamed it on her hormones.

"Casey, I need to talk to Sarah alone please," Chuck pleaded. "Well, only if it's okay with her. How can we be sure she is safe with you now?" Casey replied. "Guys (sob), I'm fine. We can talk, Chuck," Sarah interjected. This was just something she was going to have to face. Casey grunted and left the room. Chuck walked over to Sarah and got on his knees. He didn't know exactly what he wanted to say, but he knew that nothing could make up for what he just did. "Sarah, that was just the intersect. You know that, right? I could never do something like that to you. I love you. I would never hurt you," Chuck explained. "Not intentionally you wouldn't, Chuck. I do know that. But it's not always up to you anymore. It's up to that stupid computer in your head. Kind of like it's not up to me that I'm doing all this blubbering right now. It's up to my hormones," the female agent retorted. Chuck went in to comfort her again. This time, after a small wince, she was able to accept his gesture of comfort. It felt so good to be in his arms in that moment. In that moment everything was perfect. But things would never be the same. When she pulled away and looked into his eyes all she could see was the image of him pushing a gun into her forehead, but she shook the feeling off. "I have to make this right, Sarah. I can't imagine every letting things get that far again. You have to teach me. Teach me to control myself and my flashes. Then we won't have to worry about that... stuff ever happening again," said Chuck. "Okay," said Sarah, "but on one condition. I want to be with you, Chuck. I want to be your girlfriend for real. So I need you to teach me to be in a normal relationship."

They agreed that that seemed like a fair trade- off. They also agreed that the only way to seal the deal was a kiss. They both stood up and he grabbed her around the waist. She pushed her hands through his hair and her mouth against his. Everything was right in the world when they were together, and they were both excited to start learning.


End file.
